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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
2e8rSAHDiphthine synthase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2e8rSAHDiphthine synthase/1.000
2eleSAHDiphthine synthase/0.838
2huvSAHDiphthine synthase/0.808
2owgSAHDiphthine synthase/0.802
2el3SAHDiphthine synthase/0.799
2owkSAHDiphthine synthase/0.791
2eldSAHDiphthine synthase/0.787
2eh2SAHDiphthine synthase/0.780
2ehlSAHDiphthine synthase/0.775
2pcgSAHDiphthine synthase/0.768
2e7rSAHDiphthine synthase/0.767
2e4nSAHDiphthine synthase/0.761
2hutSAHDiphthine synthase/0.758
2p6dSAHDiphthine synthase/0.750
2ek4SAHDiphthine synthase/0.737
2emuSAHDiphthine synthase/0.736
2p9dSAHDiphthine synthase/0.732
2dv5SAHDiphthine synthase/0.731
2emrSAHDiphthine synthase/0.727
2e15SAHDiphthine synthase/0.725
2pckSAHDiphthine synthase/0.725
2ek3SAHDiphthine synthase/0.720
2pcaSAHDiphthine synthase/0.717
2pb6SAHDiphthine synthase/0.714
2eh5SAHDiphthine synthase/0.711
2ekaSAHDiphthine synthase/0.710
2huqSAHDiphthine synthase/0.708
2p5fSAHDiphthine synthase/0.708
2ek2SAHDiphthine synthase/0.703
2eh4SAHDiphthine synthase/0.693
2eniSAHDiphthine synthase/0.692
2pb5SAHDiphthine synthase/0.690
2dxxSAHDiphthine synthase/0.689
2p5cSAHDiphthine synthase/0.677
2pchSAHDiphthine synthase/0.677
2e17SAHDiphthine synthase/0.671
2ejkSAHDiphthine synthase/0.671
2dsgSAHDiphthine synthase/0.666
2e07SAHDiphthine synthase/0.660
2huxSAHDiphthine synthase/0.660
2dsiSAHDiphthine synthase/0.659
2dv7SAHDiphthine synthase/0.659
2z6rSAHDiphthine synthase/0.659
2pcmSAHDiphthine synthase/0.658
1vceSAHDiphthine synthase/0.654
2p6iSAHDiphthine synthase/0.654
2e8sSAHDiphthine synthase/0.653
2dv3SAHDiphthine synthase/0.651
2hr8SAHDiphthine synthase/0.644
2e8qSAHDiphthine synthase/0.640
2pciSAHDiphthine synthase/0.639
2dxwSAHDiphthine synthase/0.636
2dxvSAHDiphthine synthase/0.634
2p6kSAHDiphthine synthase/0.632
1wngSAHDiphthine synthase/0.631
2pb4SAHDiphthine synthase/0.630
2e08SAHDiphthine synthase/0.627
2ed5SAHDiphthine synthase/0.627
2el0SAHDiphthine synthase/0.620
2dshSAHDiphthine synthase/0.616
2egbSAHDiphthine synthase/0.616
2ek7SAHDiphthine synthase/0.615
2p2xSAHDiphthine synthase/0.610
2dv4SAHDiphthine synthase/0.604
2e8hSAHDiphthine synthase/0.604
2en5SAHDiphthine synthase/0.603
2egsSAHDiphthine synthase/0.600
2ejjSAHDiphthine synthase/0.600
2eeqSAHDiphthine synthase/0.593
2owuSAHDiphthine synthase/0.592
2e16SAHDiphthine synthase/0.589
2p6lSAHDiphthine synthase/0.582
2dekSAHDiphthine synthase/0.568
2ejzSAHDiphthine synthase/0.567
2ed3SAHDiphthine synthase/0.565
2eglSAHDiphthine synthase/0.559
2owfSAHDiphthine synthase/0.541
2owvSAHDiphthine synthase/0.540
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.518
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.506
3gw9VNILanosterol 14-alpha-demethylase/0.502
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.491
4g7gVFVLanosterol 14-alpha-demethylase/0.491
2gjlFMNNitronate monooxygenase1.13.12.160.490
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.486
2y3sTIRTamL/0.483
3zh8C58Protein kinase C iota type2.7.11.130.483
3gqvNAPEnoyl reductase LovC10.480
4wriOKAOkadaic acid binding protein 2-alpha/0.480
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.479
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.479
3vqsJT1Genome polyprotein/0.478
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.477
4g3jVNTLanosterol 14-alpha-demethylase/0.477
1me6IVSPlasmepsin-23.4.23.390.476
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
1dirNADDihydropteridine reductase1.5.1.340.474
2qbuSAHPrecorrin-2 methyltransferase/0.473
4q71FADBifunctional protein PutA/0.473
1xe55FEPlasmepsin-23.4.23.390.472
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.470
3ik6HCZGlutamate receptor 2/0.470
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.470
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.470
1bxoPP7Penicillopepsin-13.4.23.200.469
1hdrNADDihydropteridine reductase1.5.1.340.469
1lbcCYZGlutamate receptor 2/0.469
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.469
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.469
1w6hTITPlasmepsin-23.4.23.390.468
1x1aSAMC-20 methyltransferase/0.468
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.468
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
2givACOHistone acetyltransferase KAT8/0.467
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.467
2ifaFMNUncharacterized protein/0.466
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.466
1j1zATPArgininosuccinate synthase/0.465
1xe65FPPlasmepsin-23.4.23.390.465
2cgv3B3Serine/threonine-protein kinase Chk12.7.11.10.465
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.464
3slkNDPPolyketide synthase extender module 2/0.464
4djhJDCKappa-type opioid receptor/0.464
1tehNADAlcohol dehydrogenase class-31.1.1.10.463
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
1kkq471Peroxisome proliferator-activated receptor alpha/0.462
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.462
1qorNDPQuinone oxidoreductase 1/0.461
2rhgIGPTryptophan synthase alpha chain/0.461
3rsv3RSBeta-secretase 13.4.23.460.461
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.460
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.460
3s1dZIRCytokinin dehydrogenase 11.5.99.120.460
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.460
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.460
1f8wFADNADH peroxidase1.11.1.10.459
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.459
2pswCOAN-alpha-acetyltransferase 50/0.459
2y4gTIRTamL/0.459
4nbwNADShort-chain dehydrogenase/reductase SDR/0.459
1bim0QBRenin3.4.23.150.458
1f8fNADBenzyl alcohol dehydrogenase/0.458
1vikBAYGag-Pol polyprotein/0.458
1x1cSAHC-20 methyltransferase/0.458
2b53D23Cyclin-dependent kinase 22.7.11.220.458
2xhd7T9Glutamate receptor 2/0.458
4eb7PLPCysteine desulfurase IscS 2/0.458
2q5g1FAPeroxisome proliferator-activated receptor delta/0.457
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.457
4ftr5HKSerine/threonine-protein kinase Chk12.7.11.10.457
4m83ERYOleandomycin glycosyltransferase2.4.10.457
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.456
2ebaFADPutative glutaryl-CoA dehydrogenase/0.456
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.456
3ig6438Urokinase-type plasminogen activator3.4.21.730.456
3vswR31Renin3.4.23.150.456
4a83DXCMajor pollen allergen Bet v 1-A/0.456
1ma0NADAlcohol dehydrogenase class-31.1.1.10.455
2q4bNAPUncharacterized protein At5g02240/0.455
1bil0IURenin3.4.23.150.454
1tqf32PBeta-secretase 13.4.23.460.454
1xddAAYIntegrin alpha-L/0.454
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.454
2g247IGRenin3.4.23.150.454
3lzs017Gag-Pol polyprotein3.4.23.160.454
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.454
4wudANPDNA gyrase subunit B/0.454
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.454
5hwsNAP2-dehydropantoate 2-reductase/0.454
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.453
1jkx138Phosphoribosylglycinamide formyltransferase/0.453
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.453
2rlcCHDCholoylglycine hydrolase3.5.1.240.453
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.453
3uylTYDProbable NDP-rhamnosyltransferase/0.453
4bfzZVZPantothenate kinase2.7.1.330.453
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.453
1dhrNADDihydropteridine reductase1.5.1.340.452
2xfsJ01Uncharacterized protein/0.452
3u9eCOALmo1369 protein/0.452
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.452
4r20AERCytochrome P450 family 17 polypeptide 2/0.452
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.452
5cyoGDPSeptin-9/0.452
1pjcNADAlanine dehydrogenase/0.451
1udaUFGUDP-glucose 4-epimerase5.1.3.20.451
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3sf6FDAGlutaryl-CoA dehydrogenase/0.451
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.451
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.451
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.450
1rneC60Renin3.4.23.150.450
2w06FRVCyclin-dependent kinase 22.7.11.220.450
2w3bNDPDihydrofolate reductase1.5.1.30.450
3hyoADPPyridoxal kinase/0.450
3umpATPATP-dependent 6-phosphofructokinase isozyme 22.7.1.110.450
4ejmNAPPutative zinc-binding dehydrogenase/0.450
4f5yC2EStimulator of interferon genes protein/0.450
4r21STRCytochrome P450 family 17 polypeptide 2/0.450
5eb5FAD(R)-mandelonitrile lyase 14.1.2.100.450
1bwsNDPGDP-L-fucose synthase/0.449
1fm4DXCMajor pollen allergen Bet v 1-L/0.449
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.449
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.449
3ijoB4DGlutamate receptor 2/0.449
3sc13S13-phosphoinositide-dependent protein kinase 12.7.11.10.449
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.449
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.449
4xguADPPutative pachytene checkpoint protein 2/0.449
1x1dSAHC-20 methyltransferase/0.448
5dp2NAPCurF/0.448
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.447
2a1mCAMCamphor 5-monooxygenase1.14.15.10.447
2oapANPType II secretion system protein (GspE-2)/0.447
2rcyNAPPyrroline-5-carboxylate reductase/0.447
2vwqNAPGlucose 1-dehydrogenase/0.447
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.447
3raiX85Cyclin-dependent kinase 22.7.11.220.447
3tneRITCandidapepsin-13.4.23.240.447
3to6LYS_CMCHistone acetyltransferase ESA1/0.447
4a81DXCMajor pollen allergen Bet v 1-A/0.447
1mj9COAHistone acetyltransferase ESA1/0.446
1zeoC01Peroxisome proliferator-activated receptor gamma/0.446
2a94AP0L-lactate dehydrogenase1.1.1.270.446
2he5NDPAldo-keto reductase family 1 member C211.1.10.446
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.446
2znnS44Peroxisome proliferator-activated receptor alpha/0.446
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.446
3jzdNADMaleylacetate reductase/0.446
3ndcSAHPrecorrin-4 C(11)-methyltransferase2.1.1.1330.446
3orfNADDihydropteridine reductase1.5.1.340.446
4ambDUDPutative glycosyl transferase/0.446
4gkvNADAlcohol dehydrogenase, propanol-preferring1.1.1.10.446
4ig01FGGag-Pol polyprotein2.7.7.490.446
4q73FADBifunctional protein PutA/0.446
5f8eSAHPossible transcriptional regulatory protein/0.446
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.445
1rp0AHZThiamine thiazole synthase, chloroplastic/0.445
1z7yAA5Cysteine synthase 12.5.1.470.445
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.445
2g1o2IGRenin3.4.23.150.445
2ou2ACOHistone acetyltransferase KAT5/0.445
3otwCOAPhosphopantetheine adenylyltransferase/0.445
3qwbNDPProbable quinone oxidoreductase1.6.5.50.445
4dd8BATDisintegrin and metalloproteinase domain-containing protein 83.4.240.445
4l4xNDPAmphI/0.445
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.445
2cv2GSUGlutamate--tRNA ligase6.1.1.170.444
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.444
2wedPP6Penicillopepsin-13.4.23.200.444
3a3yOBNSodium/potassium-transporting ATPase subunit alpha/0.444
3vdqNAD3-hydroxybutyrate dehydrogenase/0.444
4dbzNDPPutative ketoacyl reductase1.3.10.444
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.443
1vp6CMPCyclic nucleotide-gated potassium channel mll3241/0.443
2dgnDOIAdenylosuccinate synthetase isozyme 1/0.443
2i4qUA4Renin3.4.23.150.443
2vbdV10Isopenicillin N synthase1.21.3.10.443
2zvcSAHPrecorrin-3 C17-methyltransferase/0.443
3em3478Gag-Pol polyprotein3.4.23.160.443
3f3sNADLambda-crystallin homolog/0.443
3h6vNS6Glutamate receptor 2/0.443
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.443
4pl0ANPMicrocin-J25 export ATP-binding/permease protein McjD/0.443
4yvz3ATDNA integrity scanning protein DisA/0.443
1nzfUPGDNA beta-glucosyltransferase/0.442
2a1tFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.442
2cftPLPPyridoxal phosphate phosphatase/0.442
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.442
2g1s4IGRenin3.4.23.150.442
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.442
3a1nNADNDP-sugar epimerase/0.442
3d91REMRenin3.4.23.150.442
3i25MV7Beta-secretase 13.4.23.460.442
4dptAGSMevalonate diphosphate decarboxylase/0.442
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.442
4prvADPDNA gyrase subunit B/0.442
5jscFADPutative acyl-CoA dehydrogenase/0.442
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
1udyFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.441
2b8v3BNBeta-secretase 13.4.23.460.441
2bjfDXCCholoylglycine hydrolase3.5.1.240.441
2ie0ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.441
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.441
2y8lADP5'-AMP-activated protein kinase subunit gamma-1/0.441
3bbrBHYGlutamate receptor 2/0.441
3nxxNDPDihydrofolate reductase1.5.1.30.441
3oev3OEProteasome subunit beta type-53.4.25.10.441
3oev3OEProteasome subunit beta type-63.4.25.10.441
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.441
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.441
4i1iNADMalate dehydrogenase/0.441
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.441
1cf3FADGlucose oxidase1.1.3.40.440
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.440
1jipKTN6-deoxyerythronolide B hydroxylase/0.440
1qrpHH0Pepsin A-43.4.23.10.440
1rfuADPPyridoxal kinase2.7.1.350.440
2iviACWIsopenicillin N synthase1.21.3.10.440
3tjzGNPADP-ribosylation factor 1/0.440
3zkyWT4Isopenicillin N synthase1.21.3.10.440
4gsuDWZL,D-transpeptidase 22.3.20.440